I just started playing Majora's Mask and put in about 6+ hours of gameplay. I saved my progress by using the Song of Time (no save states). Today I opened the game again only to see that there is no save file... Can anybody enlighten me on what could have happened? And if it's possible explain how to restore the save file? Thanks in advance!

The game can reset the entire save file if there is a checksum mismatch, but I think this is not a likely thing.

I think maybe the save file got moved by Vista's (or later) elevation if you changed Windows users privileges and settings any or you made changes to the game's RDB settings for the save type. Or maybe there are just new regressions in Project64 now.